libplinkio

This is a small C and Python library for reading Plink genotype files.

Currently it can:

Read and parse BED, BIM and FAM files.
Transpose BED files.
Write BED, BIM and FAM files.

Libplinkio will reach 1.0 when it can:

Read PED files (i.e. non-binary bed-files).

Project rationales:

Use C to make it as simple as possible to add bindings for other languages.
Focus only on IO-functionality.
Few external dependencies to make it easy to use.

Installing

Installing this library is easy, just configure and make. This will also install Python bindings for the active interpeter.

NEWS The python extension can now be installed by

pip install plinkio

Installing to a standard location

mkdir build
cd build
../configure
make && make check && sudo make install

You can also pass the --disable-tests flag to configure to avoid building the unit tests and the dependency to libcmockery. Note howerver, in this case make check will not do anything.

Installing to a custom location

mkdir build
cd build
../configure --prefix=/path/to/plinkio
make && make check && make install

Linking to your program

To link your own application to libplinkio you can use the following include and library paths after installing it:

gcc -lplinkio source.c

If you installed libplinkio to a custom location you need to specify the location of libplinkio:

gcc -lplinkio -I/path/to/plinkio/include -L/path/to/plinkio/lib source.c

Genotype coding

The genotypes are coded 0, 1, 2, and 3. The numbers 0-2 represent the number of A2 alleles as specified in the .bim file. The number 3 represents a missing genotype.

Using in C

For specific information look at http://mfranberg.github.com/libplinkio/index.html

The following C program prints the genotypes of all individuals. Note, that it is not recommended to run this program on a big plink file since it will fill your screen with data.

#include <stdlib.h>
#include <stdio.h>
#include <plinkio/plinkio.h>

int
main(int argc, char *argv[])
{   
    struct pio_file_t plink_file;
    snp_t *snp_buffer;
    int sample_id;
    int locus_id;

    if( pio_open( &plink_file, argv[ 1 ] ) != PIO_OK )
    {
        printf( "Error: Could not open %s\n", argv[ 1 ] );
        return EXIT_FAILURE;
    }

    if( !pio_one_locus_per_row( &plink_file ) )
    {
        printf( "This script requires that snps are rows and samples columns.\n" );
        return EXIT_FAILURE;
    }

    locus_id = 0;
    snp_buffer = (snp_t *) malloc( pio_row_size( &plink_file ) );
    while( pio_next_row( &plink_file, snp_buffer ) == PIO_OK )
    {
        for( sample_id = 0; sample_id < pio_num_samples( &plink_file ); sample_id++)
        {
            struct pio_sample_t *sample = pio_get_sample( &plink_file, sample_id );
            struct pio_locus_t *locus = pio_get_locus( &plink_file, locus_id );
            printf( "Individual %s has genotype %d for snp %s.\n", sample->iid, snp_buffer[ sample_id ], locus->name );
        }

        locus_id++;
    }

    free( snp_buffer );
    pio_close( &plink_file );
    
    return EXIT_SUCCESS;
}

Accessing sample and locus information in C

Information about samples and loci are obtained by referencing directly into the struct. The fields are summarized below.

The pio_sample_t declaration

/**
 * Data structure that contains the PLINK information about a sample (individual).
 */
struct pio_sample_t
{
    /**
     * An internal reference id, so that we can read them in order.
     */
    size_t pio_id;

    /**
     * Family identifier.
     */
    char *fid;

    /**
     * Plink individual identifier.
     */
    char *iid;

    /**
     * Plink individual identifier of father, 0 if none.
     */
    char *father_iid;

    /**
     * Plink individual identifier of mother, 0 if none.
     */
    char *mother_iid;

    /**
     * The sex of the individual.
     */
    enum sex_t sex;

    /**
     * Affection of the individuals, case, control or unkown. Control
     * is always 0 and case always 1.
     */
    enum affection_t affection;

    /**
     * A continuous phenotype of the individual.
     */
    float phenotype;
};

The pio_locus_t declaration

/**
 * Data structure that contains the PLINK information about a locus (SNP).
 */
struct pio_locus_t
{
    /**
     * An internal reference id, so that we can read them in order.
     */
    size_t pio_id;

    /**
     * Chromosome number starting from 1.
     */
    unsigned char chromosome;

    /**
     * Name of the SNP.
     */
    char *name;

    /**
     * Genetic position of the SNP.
     */
    float position;

    /**
     * Base pair position of the SNP.
     */
    long long bp_position;

    /**
     * First allele.
     */
    char *allele1;

    /**
     * Second allele.
     */
    char *allele2;
};

Using in Python

The following script does the same as the above C program, utilizing most of the API.

from plinkio import plinkfile

plink_file = plinkfile.open( "/path/to/plink_file" )
if not plink_file.one_locus_per_row( ):
     print( "This script requires that snps are rows and samples columns." )
     exit( 1 )

sample_list = plink_file.get_samples( )
locus_list = plink_file.get_loci( )

for locus, row in zip( locus_list, plink_file ):
    for sample, genotype in zip( sample_list, row ):
        print( "Individual {0} has genotype {1} for snp {2}.".format( sample.iid, genotype, locus.name ) )

Accessing sample and locus information in Python

The file API

##
# Opens the plink file at the given path.
#
# @param path The prefix for a .bed, .fam and .bim without
#             the extension. E.g. for the files /plink/myfile.fam,
#             /plink/myfile.bim, /plink/myfile.bed use the path
#             /plink/myfile
#
def open(path):
    pass

##
# Creates a new plink file based on the given samples.
#
# @param path The prefix for a .bed, .fam and .bim without
#             the extension. E.g. for the files /plink/myfile.fam,
#             /plink/myfile.bim, /plink/myfile.bed use the path
#             /plink/myfile
# @param samples A list of Sample objects to write to the file.
#
def create(path, samples):
    pass

The Sample object

class Sample:
    def __init__(self, fid, iid, father_iid, mother_iid, sex, affection, phenotype = 0.0):
        ##
        # Family id.
        #
        self.fid = fid

        ##
        # Individual id.
        #
        self.iid = iid

        ##
        # Individual id of father.
        #
        self.father_iid = father_iid

        ##
        # Individual id of mother.
        #
        self.mother_iid = mother_iid

        ##
        # Sex of individual.
        #
        self.sex = sex

        ##
        # Affection of individual, 0/1, control/case
        #
        self.affection = affection

        ##
        # Optional continuous phenotype, will be 0.0/1.0 if control/case
        #
        self.phenotype = phenotype

The Locus object

class Locus:
    def __init__(self, chromosome, name, position, bp_position, allele1, allele2):
        ##
        # Chromosome number starting from 1
        #
        self.chromosome = chromosome

        ##
        # Name of the loci, usually rs-number or
        # chrX:pos.
        #
        self.name = name

        ##
        # Genetic position (floating point number).
        #
        self.position = position

        ##
        # Base pair position (integer).
        #
        self.bp_position = bp_position

        ##
        # First allele
        #
        self.allele1 = allele1

        ##
        # Second allele
        #
        self.allele2 = allele2

The PlinkFile object

class PlinkFile:
    ##
    # Returns the prefix path to the plink file, e.g.
    # without .bim, .bed or .fam.
    #
    def get_path():
        pass

    ##
    # Returns a list of the Sample objects.
    #
    def get_samples():
        pass

    ##
    # Returns a list of Locus objects.
    #
    def get_loci():
        pass

    ##
    # Determines how the snps are stored. It will return
    # true if a row contains the genotypes of all individuals
    # from a single locus, false otherwise.
    #
    def one_locus_per_row():
        pass

    ##
    # Closes the file.
    #
    def close():
        pass

    ##
    # Transposes the file.
    #
    # @param new_path Prefix of the new plink file.
    #
    def transpose(new_path):
        pass

The WritablePlinkFile object

class WritablePlinkFile: 
    ##
    # Returns a list of Sample objects.
    #
    def get_samples():
        pass

    ##
    # Returns a list of Locus objects written so far.
    #
    def get_loci():
        pass

    ##
    # Takes a locus and the corresponding genotypes and
    # writes them to the plink file.
    # 
    # @param locus A Locus object to write.
    # @param row An indexable list of genotypes.
    #
    def write_row(locus, row):
        pass
    
    ##
    # Closes the file.
    #
    def close():
        pass

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